Unexpected
by AmethystPearl99
Summary: An alteration closed to the ending of Rebellion. Homura was willing to go with Madoka after her soul gem was purified but the girls have not destroyed every last Incubators. Now that Madoka has reveal herself, the Incubators plan to turn the magical girls back into witches while hurting Homura even more...by taking Madoka. Rated T just to be safe.
1. Chapter 1: The Captured Goddess

**Hello Madoka Magica fans. I am YellowPearl07 for those who don't know me. I have re-watch Rebellion and then an idea came to my head. What if Homura did not became the devil/akuma? What if the Incubators were not completely destroyed? It lead me to write this. I do not own Puella Magi Madoka Magica or their characters, just my plot. I hoped you enjoy reading it.  
**

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Chapter 1: The Captured Goddess

Finally, Homura can see Madoka again. As Madoka descended from the sky, the carriage Sayaka and Nagisa are in is driven closer to the Earth. Sayaka is driving the carriage as Nagisa is blowing bubbles.

"Now, let's go. We'll always be together from now on." Madoka told her as she was closer to purify her tainted soul gem.

Suddenly, red crystals popped up on the ground as Madoka is taking the grief from Homura's soul gem. The red crystals started to shocked Madoka, interrupting the process.

"Madoka!" Homura exclaimed.

"W-what is going on?" Sayaka asked in alarm as the carriage began to tipped over causing both her and Nagisa to fall out of it.

Mami summoned her percussion-lock rifled musket while Kyoko summoned her spear.

"Did you thought that you have gotten rid of us completely? Human thoughts are so irrational...to think that you could win." Kyubey spoke out loud as many red eyes glowed in the dark.

"Incubator!" Homura exclaimed in disgust.

"Really, did you thought that it was over? You didn't even know that you were the bigger trap set for Kaname Madoka, speaking of which, those crystals were set up to capture the goddess of this universe. We have this planned out just in case if the isolation field was destroyed." Kyubey explained.

The red crystals continue to shock Madoka as she screams in pain.

"It's too much! These crystals...it's taking my powers away!" Madoka screamed. She started to fall as she disappeared in a flash of light in front of Homura.

"Madoka!" Homura yelled in disbelief.

Kyoko pointed her spear at Kyubey. "What do you do?! Where is she?! Where did she go?!" she demand angrily.

"Those crystals absorbed her powers, but don't worry. It will just cause her to be unconscious for a little while so don't waste your time fighting. She is already in our care. As long as she cooperates with us, nothing will harm her." Kyubey told the girls with no care at all.

"Why you little-" Kyoko began as she attempt to attack him. However, he disappeared before her spear could land a hit on him, along with the other Incubators.

Homura was on her knees, feeling devastated as tears fall from her eyes.

 _'It seems that no matter what universe I'm in, I can never be able to protect her just when I got the chance to do so.'_

Homura opened her palm to reveal her cleansed soul gem.

"Madoka." she said her name.

Mami went to help Nagisa and Sayaka from the now broken carriage. Sayaka walked up to Homura.

"What are you doing? Are you just going to sit here while the Incubators have their hold onto Madoka? Who knows what they could be doing to her!" Sayaka asked her in frustration.

Homura said nothing. She felt that nothing could changed her back to the shy but happy girl she used to be. She is still the emotionless girl who have always suffered and it has only gotten worse. Just when she thought she could be happy being with her friends, but mostly Madoka, that happiness is quickly snatched away from her by those cold and selfish beings. She de-transformed to her school uniform as she got up to her feet.

"Akemi-san?" Mami called out. "Where are you going?"

"I'm going back...to Mitakihara City. After I am ready, I going to get Madoka back." Homura answered in an emotionless tone.

"But we have to stay together. Now that the Incubators have Madoka, we don't know what they could be doing next!" Sayaka exclaimed.

"You can do whatever you want, but I'm not coming with you." Homura countered as she continued to walk to the city.

"But-" Mami began.

"It's no use in trying to convince her. She won't give in. Seriously, she needs to start working together with us." Sayaka sighed as they lost sight of her.

"So, what should we do now?" Kyoko asked.

"We should probably head back too. Now that all of this has happened, we need to go back to the city. We can go at my place." Mami replied.

"Fine, but you are going to have to bake me a cake. I'm starving and I haven't eaten for a while." Kyoko complained.

"You're always hungry even at a time like this." Sayaka commented in disapproval.

"And Nagisa wants to eat cheese at Mami's place!" Nagisa exclaimed.

"Not you too..." Sayaka replied in disbelief.

-Homura's House-

At her home, Homura is still recalling what had happened. Despite the despair she is feeling right now, her soul gem is not blackening, whenever if this despair is just her in a bad mood or if it has to do with Madoka cleansing it, she does not know. She got up and went to her room to fall on her bed. A flashback of the time when she first met Madoka, her warm smile made her feel comfort, the first person to become her most dearest of friends. She touch the red ribbons on her head as she shed a tear.

"Madoka, I will save you. No matter what it takes." Homura cried as she fallen asleep.

-Incubator's Base-

In the base of the Incubator, there lies a mirror. However, this was no ordinary mirror for it has someone inside of it.

-Void-

"Where am I? What is this place?" Madoka asked herself as she walked around the void.

She was her human self. She is wearing a white dress and her short pink hair was down because she gave Homura her ribbons before she left. She wonder around the void until she saw a looking glass. She look through it to see her goddess self unconscious and the Incubator's base.

"No this can't be! That must mean..."

Madoka woke up inside the mirror! She saw that she is in her goddess form as she floats in this endless space inside the mirror.

"I knew that you'd wake up eventually, Kaname Madoka." a voice spoke suddenly.

"Incubator!" Madoka exclaimed in surprise. "Why are you doing this? Why are you causing all my friends to suffer!" she demanded.

"Because you are the key to our plan." Kyubey answered.

"What?" Madoka questioned quietly in confusion.

"We're hoping, now that we got you, we can turn the universe to the way it used to be. We are planning to have all the magical girls become witches again so we can collect the unlimited amount of energy. That way, it will be much easier than fighting wraiths." Kyubey explained.

"But that is just too cruel!" Madoka yelled. She hands pressed on the glass of the mirror.

"I'm afraid you won't have a choice. You can't get out of this mirror and even if you regain all your powers back, you can't break it." Kyubey replied in a emotionless tone. "When you are ready to help us achieve our goal, call us. We'll leave you alone for a little while." Kyubey told her as he and the others left her alone.

Madoka fell to her knees as she started to cry. She was starting to feel useless again, always depending on her friends to save her, especially Homura.

"Everyone... Homura-chan... I'm sorry. For causing all of you the trouble in rescuing me." Madoka wept inside her glass prison. "I'm so sorry."

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 **That is all for today. Write, Comment, and Review if you want. It will help me know if you want to see more of my story. I hope you have enjoyed the first chapter. I'll update this story for every third week. See you at another time.  
**


	2. Chapter 2: The Soul of Hope

**Hi everyone. Like I said, I'll update every third week. When the summers begins, I will be able to update more then usual. I want to say that in this chapter, the conversation that Sayaka and Nagisa has will be in sync with Madoka. Also, they is no action in this chapter, since I want to build the story up until it reached to a point where there is action needed. Anyway, enjoy.**

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Chapter 2: The Soul of Hope

-Incubator's Base-

The Incubators are discussing on a plan to prevent the magical girls from recusing Madoka. They have come up with the idea to create the Wraith Queen, the queen of all wraiths, just like the name implies. Of course, they would have to build her so she won't be destroyed, but that wouldn't be a problem, since they have the technology to create such a powerful being. Madoka heard about the plan through the mirror and felt troubled.

"Everyone, please be alright." she prayed.

-Mami's House-

Once they reached Mitakihara City, the girls de-transformed. Mami, Sayaka and Kyoko are in their causal outfits, and Nagisa is seen wearing a polka-dotted pink dress with sleeves, dark red leggings, along with brown shoes. Everyone else who lived in the city are being carried back by Homura's familiars. Back at Mami's place, everyone was sitting around her triangular table to discuss on a plan to get Madoka back while Mami gave each of the girls a slice of cheesecake. Nagisa and Sayaka sat on one side of the table, Kyoko sat on the another, and Mami on the last side once she finished passing out the slices.

"So," Kyoko began, taking a bite of the cake with her hand. "What is the plan to get Madoka back?"

"We have to get Madoka back without the Incubators from knowing, though I expect them to already know that we will try to get her back." Sayaka replied.

"First, I think that everyone agrees that we should try to find out where they are keeping Kaname-san before we can recuse her." Mami replied.

"Unfortunately, neither me or Sayaka know where the Incubator's base is located." Nagisa admitted, putting down her plate that still has cheesecake on it.

"Not only that, but without Madoka, if your soul gems are at its limits..." Sayaka pointed out. She knew that she doesn't have to finish her sentence.

"What about you guys? Will you be affected as well?" Kyoko questioned.

"No, Sayaka and I are already taken by the Law of Cycles, so we won't become affected if our soul gems are tainted." Nagisa explained while eating her cheesecake.

"The other who is not affected is Homura. Since her soul gem was cleanse by Madoka, it will not darkened. However, you two can still be affected, which means that we will need to find those grief cubes before we can get to Madoka." Sayaka further explained.

"Then we are at a loss and they are at the advantage. It is like putting Hope in a box while curses are being active." Mami trailed off.

"Jeez, I can't believe we are stuck at a pointless time like this!" Kyoko commented as she finished her slice.

"Sakura-san, nothing will help us if we continue to think that it is hopeless. If only Akemi-san could corporate with us..." Mami replied, thinking deeply. "If only there is a way for Kaname-san to reached us."

Nagisa and Sayaka glanced at each other. They decided to tell their friends everything on what they know.

"Actually, there might be a way." Sayaka began.

"What?" Mami asked.

"Back then, when we found out that Homura is in danger, Madoka, I, and Nagisa entered the Incubator's seal. Madoka gave us all her memories and powers, but before she did, she explained something to us." Sayaka explained.

 **-Flashback-**

In the desert of Mitakihara City, the Incubators are watching Homura, as her soul gem is building the fake city. Sayaka and Nagisa, in their magical girl outfits, and Goddess Madoka are hiding in the heavens, away from the Incubator's view.

"There it is Madoka, the Incubator's seal." Sayaka whispered.

"Homura-chan, we have to save her." Madoka whispered back in concern.

"Wait, it must be a trap Madoka! The Incubators must have captured Homura, to get to you." Sayaka reminded her.

"If you go as you are now, then they would certainly try to capture you too." Nagisa added.

"You're right, but there is still a way. Sayaka-chan, Nagisa-chan, when we enter the seal, I will entrust you both with all my powers and memories until I will need them again. However, there is something that you two will need to know. If we succeeded but something happens to me, and I ended up in the Incubator's hands, the power of my soul gem..."

 **-End of Flashback-**

-Incubator's Base-

In the mirror, Madoka wrapped herself in her thoughts until she remembered something.

 _'That's right. I told Sayaka-chan and Nagisa-chan. If that's the case, then I must do this!'_ Madoka thought.

"Kaname Madoka, are you going to try to escape? I told you, that it's useless." Kyubey reminded her as Madoka started to stand up.

"No, I know that in this state, I can't escaped even if I wanted to. However, there is a way for me to delay your plans!" Madoka exclaimed as her pink teardrop began to glow.

-Mami's House-

"What is the power of her soul gem?" Kyoko asked.

"The power that her soul gem contained..." Nagisa started.

 **-Flashback-**

"...has the ability to change its appearance." Madoka replied to Sayaka and Nagisa.

"What do you mean by that, Madoka?" Nagisa asked in curiosity.

"My soul gem has to power to change it's shape. Normally, everyone's soul is what they would looked like. However, my soul gem is different. It is split between myself as Kaname Madoka, a normal middle school girl and the me now, who brings all magical girls their hope." Madoka explained to her friends as she touched her teardrop gem. "Now, lets go and save Homura-chan."

 **-Flashback Ends-**

"It can...changed forms?" Mami questioned.

"Yes. Now that Madoka has taken different forms, so has her soul gem. It lies in between." Nagisa finished as she put down her empty plate.

"If that is so and her soul gem can take the form of a magical girl, then who is she?" Kyoko asked.

-Incubator's Base-

"Kaname Madoka, what are you planning?" Kyubey questioned.

"There is a secret that I know concerning my own soul gem. I knew that I might get caught by you, so that is why I'm going to do this. To prevent you from knowing what my intentions are, I will not tell you." Madoka exclaimed.

She placed her soul gem near to the glass where it began to glow even brighter, blinding every Incubators in light. A tiny piece of light went out of Madoka's soul gem and out of the mirror. It changed form as a tiny pink butterfly and fluttered away. Madoka passed out as the light disappeared. She knew that this would happen but didn't care. Releasing the light of her soul gem is similar like the soul leaving the body. It is exactly the same way when normal girls become magical girls, needing to keep their soul gems close to them. The difference is, in this case, even though it is close to her, without the complete radiance of her soul gem, the same effects happens. The goddess is now asleep in hope that a part of her soul could find her friends, defeat the Incubators once and for all, and reuniting with that piece again, bringing her back.

 _'They already know, the name of the light of my soul gem...She is the same as me and I am the same as her.'_ Madoka thought as she closed her eyes.

-Mami's House-

"The name of the soul gem that will taken form as a magical girl, her name is... Rose." Sayaka answered.

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 **I hope that you enjoy this chapter. The idea of Madoka's soul gem taken a new form is inspired by how the girls' soul become soul gems and the scene where Homura took a 'part of Madoka'. Lastly, in the opening series, I wanted the spirit part of Madoka that has long hair who allowed her to transform named Rose, since her bow has a rose on top. Write, Comment, Review, and asked Questions if you have one. Also, if you have suggestions, please tell me. I would love to hear what creative ideas you might have. See you on the last week of June.**


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